Description Usage Arguments Details Author(s) See Also

View source: R/patchwork.copynumbers.r

Input data for this function should be assessed from any of the karyotype_chroms() plots. For example <yoursample>_karyotype.chr<1-22,X,Y>.png.

See argument details.

1 | ```
patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F,male.sample=F,male2femref=F)
``` |

`CNfile` |
The name and path of your copynumbers file, generated from patchwork.plot(). Example Myfile_copynumbers.Rdata. |

`cn2` |
The approximate position of copy number 2,diploid, on total intensity / coverage axis. |

`delta` |
The difference in total intensity between consecutive copy numbers. For example 1 and 2 or 2 and 3. If copy number 2 has total intensity ~0.6 and copy number 3 har total intensity ~0.8 then delta would be 0.2. |

`het` |
Allelic imbalance ratio of heterozygous copy number 2. |

`hom` |
Allelic imbalance ratio of Loss-of-heterozygosity copy number 2. |

`maxCn` |
Highest copy number to calculate for. Default is 8. |

`ceiling` |
Default is 1. |

`forcedelta` |
Default is FALSE. If TRUE the delta value will not be subject to small adjustment changes. |

`male.sample` |
Default is FALSE. If it is a male sample put TRUE here and it will handle the XY chromosomes better. |

`male2femref` |
Default is FALSE. If TRUE the sample is male but the reference you used is female. This will correct for this. |

1. Run the patchwork.plot correctly. This will generate <yourfile>_copynumbers.Rdata. 2. View your plots and decide the correct parameters for the other arguments of this function. 4. Run the function.

Markus Mayrhofer, [email protected] Sebastian DiLorenzo, [email protected]

`patchwork.plot`

`subfunctions_copynumbers`

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